Metal ion dependence, thermodynamics, and kinetics for intramolecular docking of a GAAA tetraloop and receptor connected by a flexible linker

Biochemistry
Christopher D DowneyArthur Pardi

Abstract

The GAAA tetraloop-receptor motif is a commonly occurring tertiary interaction in RNA. This motif usually occurs in combination with other tertiary interactions in complex RNA structures. Thus, it is difficult to measure directly the contribution that a single GAAA tetraloop-receptor interaction makes to the folding properties of a RNA. To investigate the kinetics and thermodynamics for the isolated interaction, a GAAA tetraloop domain and receptor domain were connected by a single-stranded A(7) linker. Fluorescence resonance energy transfer (FRET) experiments were used to probe intramolecular docking of the GAAA tetraloop and receptor. Docking was induced using a variety of metal ions, where the charge of the ion was the most important factor in determining the concentration of the ion required to promote docking {[Co(NH(3))(6)(3+)] < [Ca(2+)], [Mg(2+)], [Mn(2+)] < [Na(+)], [K(+)]}. Analysis of metal ion cooperativity yielded Hill coefficients of approximately 2 for Na(+)- or K(+)-dependent docking versus approximately 1 for the divalent ions and Co(NH(3))(6)(3+). Ensemble stopped-flow FRET kinetic measurements yielded an apparent activation energy of 12.7 kcal/mol for GAAA tetraloop-receptor docking. RNA constructs with U(7) ...Continue Reading

References

Jul 30, 1990·Journal of Molecular Biology·J D PuglisiI Tinoco
Jan 25, 1993·Nucleic Acids Research·B StreicherR Schroeder
Feb 11, 1994·Journal of Molecular Biology·F L Murphy, T R Cech
Oct 10, 1997·Nucleic Acids Research·K J YoungJ A Grasby
Feb 21, 1998·The EMBO Journal·S E ButcherJ Feigon
Aug 26, 1998·Journal of Molecular Biology·M S RookJ R Williamson
Nov 5, 1999·Journal of Molecular Biology·I Tinoco, C Bustamante
May 10, 2000·Nature Structural Biology·K L BuchmuellerK M Weeks
Jun 17, 2000·Science·X ZhuangS Chu
Jun 29, 2000·Annual Review of Biochemistry·P B Moore
Aug 29, 2000·Science·T R Cech
Sep 22, 2000·Biochemistry·M L DerasS A Woodson
Oct 4, 2000·Biochemistry·S K SilvermanT R Cech
Jan 5, 2001·Nucleic Acids Research·L JaegerN B Leontis
Mar 10, 2001·RNA·S K Silverman, T R Cech
Apr 11, 2001·Proceedings of the National Academy of Sciences of the United States of America·P NissenT A Steitz
Jun 19, 2001·Current Opinion in Structural Biology·D K Treiber, J R Williamson
Apr 4, 2002·Proceedings of the National Academy of Sciences of the United States of America·Harold D KimSteven Chu
Apr 17, 2002·Journal of Molecular Biology·Vinod K Misra, David E Draper
May 23, 2002·RNA·Timothy J Wilson, David M J Lilley
Jul 12, 2002·Nature·Jennifer A Doudna, Thomas R Cech
Jul 12, 2002·Nature·Peter B Moore, Thomas A Steitz
Aug 31, 2002·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Anna Marie Pyle
Feb 8, 2003·Proceedings of the National Academy of Sciences of the United States of America·Patrizia Alberti, Jean-Louis Mergny
Mar 1, 2003·Nature·Andrey S KrasilnikovAlfonso Mondragón
Jul 19, 2003·Proceedings of the National Academy of Sciences of the United States of America·Gregory BokinskyXiaowei Zhuang
Jul 26, 2003·Nature Structural Biology·Anastasia KhvorovaSumedha D Jayasena
Oct 12, 2004·Nature Structural & Molecular Biology·Michelle K NahasTaekjip Ha
Mar 9, 2005·Trends in Biochemical Sciences·Nadrian C Seeman

❮ Previous
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Citations

Aug 7, 2013·Quarterly Reviews of Biophysics·Julie L Fiore, David J Nesbitt
Mar 28, 2012·Biochemistry·Erik D HolmstromDavid J Nesbitt
May 2, 2008·Proceedings of the National Academy of Sciences of the United States of America·Xiaohui QuNorbert F Scherer
Feb 7, 2012·Proceedings of the National Academy of Sciences of the United States of America·Julie L FioreDavid J Nesbitt
Nov 8, 2008·Nucleic Acids Research·Mark A DitzlerNils G Walter
Jun 4, 2008·Annual Review of Biochemistry·Pan T X LiIgnacio Tinoco
Mar 3, 2010·Annual Review of Biophysics·Sarah A Woodson
Nov 23, 2006·RNA·Jared H DavisSamuel E Butcher
May 18, 2007·RNA·Rahul Tyagi, David H Mathews
Nov 6, 2007·Frontiers in Bioscience : a Journal and Virtual Library·Rick Russell
May 23, 2014·Proceedings of the National Academy of Sciences of the United States of America·Nicholas F DupuisDavid J Nesbitt
May 12, 2009·Journal of Molecular Biology·Dominic LambertDavid E Draper
Jun 13, 2008·Current Opinion in Structural Biology·Hashim M Al-Hashimi, Nils G Walter
Jul 17, 2012·Journal of Molecular Biology·Julie L FioreDavid J Nesbitt
Oct 11, 2008·Journal of Molecular Biology·Kirk A Vander MeulenSamuel E Butcher
Feb 18, 2010·Chemical Physics Letters·Krishanthi S Karunatilaka, David Rueda
Jan 27, 2015·The Journal of Physical Chemistry. B·Erik D HolmstromDavid J Nesbitt
Dec 11, 2013·Physical Chemistry Chemical Physics : PCCP·Zhaojian HeShi-Jie Chen
Aug 6, 2016·Proceedings of the National Academy of Sciences of the United States of America·Namita BisariaDaniel Herschlag
Aug 26, 2017·Proceedings of the National Academy of Sciences of the United States of America·Namita BisariaDaniel Herschlag
Dec 9, 2017·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Michèle C EratRoland K O Sigel
Jan 1, 2010·The Journal of Physical Chemistry Letters·Erik D Holmstrom, David J Nesbitt
Dec 10, 2020·The Journal of Physical Chemistry. B·David A NicholsonDavid J Nesbitt
Oct 11, 2016·The Journal of Physical Chemistry. B·Abhigyan SenguptaDavid J Nesbitt
Jul 10, 2007·Journal of the American Chemical Society·Christopher D DowneyArthur Pardi
Apr 17, 2012·Cell·Reza BehrouziSarah A Woodson

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